Goal: Do an MDS plot using Irene’s SNPs to look for relatedness among plants
First, need to call SNPs using all BAM files at once:
working in directory 2019/IreneSnps on whitney
first, sort bams
for f in SNPanalysis/*LT*rmdup.bam
do
newname=`basename $f .bam`_sort.bam
samtools sort -o $newname --reference SNPanalysis/Pinsaporeference1 $f
done
next, assign read groups to bams
input=""
for f in `ls *sort.bam`
do
rg=`basename $f _rmdup_sort.bam`
input="$input -b $f -r $rg -s $rg"
done
echo $input
bamaddrg $input > LT_rmdup_sort_combined.bam
samtools index LT_rmdup_sort_combined.bam
freebayes -f SNPanalysis/Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf &
try parallel
ulimit -n 4000
/usr/local/stow/freebayes/scripts/fasta_generate_regions.py Pinsaporeference1.fai 100000 > regions
./freebayes-parallel regions 8 -f Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf
(note: I edited the freebayes-parallel script so that it would work…)
Freeybayes parallel takes about 12 hours
scp whitney.plb.ucdavis.edu:2019/IreneSnps/LT.vcf.gz ../input/
library(tidyverse)
get the vcf header
vcf.header <- system("zgrep '#C' ../input/LT.vcf.gz",intern = TRUE)
vcf.header
[1] "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t38LTR\t42LTR\t42LTRR\t43LTR\t43LTRR\t49LTWR\t49LTWRR\t95LTWR\t95LTWRR\t99LTWR"
vcf.header <- vcf.header %>%
str_replace("#","") %>% #get rid of the pound sign
str_split(pattern = "\t") %>% #split on the tabs
magrittr::extract2(1)
vcf.header
[1] "CHROM" "POS" "ID" "REF" "ALT" "QUAL" "FILTER" "INFO" "FORMAT" "38LTR" "42LTR" "42LTRR" "43LTR" "43LTRR" "49LTWR" "49LTWRR"
[17] "95LTWR" "95LTWRR" "99LTWR"
get the data
snps <- read_tsv("../input/LT.vcf.gz", na = c("","NA","."),comment="#",col_names = vcf.header) %>%
select(-ID, -FILTER) # these are empty columns
Parsed with column specification:
cols(
CHROM = col_character(),
POS = col_integer(),
ID = col_character(),
REF = col_character(),
ALT = col_character(),
QUAL = col_double(),
FILTER = col_character(),
INFO = col_character(),
FORMAT = col_character(),
`38LTR` = col_character(),
`42LTR` = col_character(),
`42LTRR` = col_character(),
`43LTR` = col_character(),
`43LTRR` = col_character(),
`49LTWR` = col_character(),
`49LTWRR` = col_character(),
`95LTWR` = col_character(),
`95LTWRR` = col_character(),
`99LTWR` = col_character()
)
|================= | 11% 44 MB
|================= | 11% 44 MB
|================= | 11% 44 MB
|================= | 11% 45 MB
|================= | 11% 45 MB
|================= | 11% 46 MB
|================= | 11% 46 MB
|================== | 11% 46 MB
|================== | 11% 47 MB
|================== | 11% 47 MB
|================== | 12% 47 MB
|================== | 12% 48 MB
|================== | 12% 48 MB
|================== | 12% 49 MB
|=================== | 12% 49 MB
|=================== | 12% 49 MB
|=================== | 12% 50 MB
|=================== | 12% 50 MB
|=================== | 12% 51 MB
|=================== | 12% 51 MB
|==================== | 12% 51 MB
|==================== | 13% 52 MB
|==================== | 13% 52 MB
|==================== | 13% 53 MB
|==================== | 13% 53 MB
|==================== | 13% 53 MB
|==================== | 13% 54 MB
|===================== | 13% 54 MB
|===================== | 13% 54 MB
|===================== | 13% 55 MB
|===================== | 13% 55 MB
|===================== | 14% 56 MB
|===================== | 14% 56 MB
|===================== | 14% 56 MB
|====================== | 14% 57 MB
|====================== | 14% 57 MB
|====================== | 14% 57 MB
|====================== | 14% 58 MB
|====================== | 14% 58 MB
|====================== | 14% 59 MB
|====================== | 14% 59 MB
|======================= | 15% 59 MB
|======================= | 15% 60 MB
|======================= | 15% 60 MB
|======================= | 15% 61 MB
|======================= | 15% 61 MB
|======================= | 15% 61 MB
|======================== | 15% 62 MB
|======================== | 15% 62 MB
|======================== | 15% 63 MB
|======================== | 15% 63 MB
|======================== | 15% 63 MB
|======================== | 16% 64 MB
|======================== | 16% 64 MB
|========================= | 16% 64 MB
|========================= | 16% 65 MB
|========================= | 16% 65 MB
|========================= | 16% 66 MB
|========================= | 16% 66 MB
|========================= | 16% 66 MB
|========================= | 16% 67 MB
|========================== | 16% 67 MB
|========================== | 17% 68 MB
|========================== | 17% 68 MB
|========================== | 17% 68 MB
|========================== | 17% 69 MB
|========================== | 17% 69 MB
|=========================== | 17% 69 MB
|=========================== | 17% 70 MB
|=========================== | 17% 70 MB
|=========================== | 17% 71 MB
|=========================== | 17% 71 MB
|=========================== | 18% 71 MB
|=========================== | 18% 72 MB
|============================ | 18% 72 MB
|============================ | 18% 73 MB
|============================ | 18% 73 MB
|============================ | 18% 73 MB
|============================ | 18% 74 MB
|============================ | 18% 74 MB
|============================ | 18% 74 MB
|============================= | 18% 75 MB
|============================= | 18% 75 MB
|============================= | 19% 76 MB
|============================= | 19% 76 MB
|============================= | 19% 76 MB
|============================= | 19% 77 MB
|============================= | 19% 77 MB
|============================== | 19% 78 MB
|============================== | 19% 78 MB
|============================== | 19% 78 MB
|============================== | 19% 79 MB
|============================== | 19% 79 MB
|============================== | 20% 79 MB
|=============================== | 20% 80 MB
|=============================== | 20% 80 MB
|=============================== | 20% 81 MB
|=============================== | 20% 81 MB
|=============================== | 20% 81 MB
|=============================== | 20% 82 MB
|=============================== | 20% 82 MB
|================================ | 20% 83 MB
|================================ | 20% 83 MB
|================================ | 21% 83 MB
|================================ | 21% 84 MB
|================================ | 21% 84 MB
|================================ | 21% 84 MB
|================================ | 21% 85 MB
|================================= | 21% 85 MB
|================================= | 21% 86 MB
|================================= | 21% 86 MB
|================================= | 21% 86 MB
|================================= | 21% 87 MB
|================================= | 21% 87 MB
|================================= | 22% 87 MB
|================================== | 22% 88 MB
|================================== | 22% 88 MB
|================================== | 22% 89 MB
|================================== | 22% 89 MB
|================================== | 22% 89 MB
|================================== | 22% 90 MB
|================================== | 22% 90 MB
|=================================== | 22% 91 MB
|=================================== | 22% 91 MB
|=================================== | 23% 91 MB
|=================================== | 23% 92 MB
|=================================== | 23% 92 MB
|=================================== | 23% 92 MB
|==================================== | 23% 93 MB
|==================================== | 23% 93 MB
|==================================== | 23% 94 MB
|==================================== | 23% 94 MB
|==================================== | 23% 94 MB
|==================================== | 23% 95 MB
|==================================== | 23% 95 MB
|===================================== | 24% 95 MB
|===================================== | 24% 96 MB
|===================================== | 24% 96 MB
|===================================== | 24% 97 MB
|===================================== | 24% 97 MB
|===================================== | 24% 97 MB
|===================================== | 24% 98 MB
|====================================== | 24% 98 MB
|====================================== | 24% 99 MB
|====================================== | 24% 99 MB
|====================================== | 25% 99 MB
|====================================== | 25% 100 MB
|====================================== | 25% 100 MB
|====================================== | 25% 100 MB
|======================================= | 25% 101 MB
|======================================= | 25% 101 MB
|======================================= | 25% 102 MB
|======================================= | 25% 102 MB
|======================================= | 25% 102 MB
|======================================= | 25% 103 MB
|======================================== | 25% 103 MB
|======================================== | 26% 104 MB
|======================================== | 26% 104 MB
|======================================== | 26% 104 MB
|======================================== | 26% 105 MB
|======================================== | 26% 105 MB
|======================================== | 26% 105 MB
|========================================= | 26% 106 MB
|========================================= | 26% 106 MB
|========================================= | 26% 107 MB
|========================================= | 26% 107 MB
|========================================= | 27% 107 MB
|========================================= | 27% 108 MB
|========================================= | 27% 108 MB
|========================================== | 27% 109 MB
|========================================== | 27% 109 MB
|========================================== | 27% 109 MB
|========================================== | 27% 110 MB
|========================================== | 27% 110 MB
|========================================== | 27% 110 MB
|========================================== | 27% 111 MB
|=========================================== | 27% 111 MB
|=========================================== | 28% 112 MB
|=========================================== | 28% 112 MB
|=========================================== | 28% 112 MB
|=========================================== | 28% 113 MB
|=========================================== | 28% 113 MB
|============================================ | 28% 114 MB
|============================================ | 28% 114 MB
|============================================ | 28% 114 MB
|============================================ | 28% 115 MB
|============================================ | 28% 115 MB
|============================================ | 29% 116 MB
|============================================ | 29% 116 MB
|============================================= | 29% 116 MB
|============================================= | 29% 117 MB
|============================================= | 29% 117 MB
|============================================= | 29% 117 MB
|============================================= | 29% 118 MB
|============================================= | 29% 118 MB
|============================================= | 29% 119 MB
|============================================== | 29% 119 MB
|============================================== | 30% 119 MB
|============================================== | 30% 120 MB
|============================================== | 30% 120 MB
|============================================== | 30% 121 MB
|============================================== | 30% 121 MB
|=============================================== | 30% 121 MB
|=============================================== | 30% 122 MB
|=============================================== | 30% 122 MB
|=============================================== | 30% 122 MB
|=============================================== | 30% 123 MB
|=============================================== | 31% 123 MB
|=============================================== | 31% 124 MB
|================================================ | 31% 124 MB
|================================================ | 31% 124 MB
|================================================ | 31% 125 MB
|================================================ | 31% 125 MB
|================================================ | 31% 126 MB
|================================================ | 31% 126 MB
|================================================ | 31% 126 MB
|================================================= | 31% 127 MB
|================================================= | 31% 127 MB
|================================================= | 32% 128 MB
|================================================= | 32% 128 MB
|================================================= | 32% 128 MB
|================================================= | 32% 129 MB
|================================================== | 32% 129 MB
|================================================== | 32% 129 MB
|================================================== | 32% 130 MB
|================================================== | 32% 130 MB
|================================================== | 32% 131 MB
|================================================== | 32% 131 MB
|================================================== | 33% 131 MB
|=================================================== | 33% 132 MB
|=================================================== | 33% 132 MB
|=================================================== | 33% 133 MB
|=================================================== | 33% 133 MB
|=================================================== | 33% 133 MB
|=================================================== | 33% 134 MB
|==================================================== | 33% 134 MB
|==================================================== | 33% 135 MB
|==================================================== | 33% 135 MB
|==================================================== | 34% 135 MB
|==================================================== | 34% 136 MB
|==================================================== | 34% 136 MB
|==================================================== | 34% 137 MB
|===================================================== | 34% 137 MB
|===================================================== | 34% 137 MB
|===================================================== | 34% 138 MB
|===================================================== | 34% 138 MB
|===================================================== | 34% 139 MB
|===================================================== | 34% 139 MB
|===================================================== | 35% 139 MB
|====================================================== | 35% 140 MB
|====================================================== | 35% 140 MB
|====================================================== | 35% 141 MB
|====================================================== | 35% 141 MB
|====================================================== | 35% 141 MB
|====================================================== | 35% 142 MB
|======================================================= | 35% 142 MB
|======================================================= | 35% 142 MB
|======================================================= | 35% 143 MB
|======================================================= | 36% 143 MB
|======================================================= | 36% 144 MB
|======================================================= | 36% 144 MB
|======================================================= | 36% 144 MB
|======================================================== | 36% 145 MB
|======================================================== | 36% 145 MB
|======================================================== | 36% 146 MB
|======================================================== | 36% 146 MB
|======================================================== | 36% 146 MB
|======================================================== | 36% 147 MB
|======================================================== | 37% 147 MB
|========================================================= | 37% 148 MB
|========================================================= | 37% 148 MB
|========================================================= | 37% 148 MB
|========================================================= | 37% 149 MB
|========================================================= | 37% 149 MB
|========================================================= | 37% 150 MB
|========================================================== | 37% 150 MB
|========================================================== | 37% 150 MB
|========================================================== | 37% 151 MB
|========================================================== | 37% 151 MB
|========================================================== | 38% 151 MB
|========================================================== | 38% 152 MB
|========================================================== | 38% 152 MB
|=========================================================== | 38% 153 MB
|=========================================================== | 38% 153 MB
|=========================================================== | 38% 153 MB
|=========================================================== | 38% 154 MB
|=========================================================== | 38% 154 MB
|=========================================================== | 38% 155 MB
|============================================================ | 38% 155 MB
|============================================================ | 39% 155 MB
|============================================================ | 39% 156 MB
|============================================================ | 39% 156 MB
|============================================================ | 39% 157 MB
|============================================================ | 39% 157 MB
|============================================================ | 39% 157 MB
|============================================================= | 39% 158 MB
|============================================================= | 39% 158 MB
|============================================================= | 39% 159 MB
|============================================================= | 39% 159 MB
|============================================================= | 40% 159 MB
|============================================================= | 40% 160 MB
|============================================================= | 40% 160 MB
|============================================================== | 40% 160 MB
|============================================================== | 40% 161 MB
|============================================================== | 40% 161 MB
|============================================================== | 40% 162 MB
|============================================================== | 40% 162 MB
|============================================================== | 40% 162 MB
|=============================================================== | 40% 163 MB
|=============================================================== | 41% 163 MB
|=============================================================== | 41% 164 MB
|=============================================================== | 41% 164 MB
|=============================================================== | 41% 164 MB
|=============================================================== | 41% 165 MB
|=============================================================== | 41% 165 MB
|================================================================ | 41% 166 MB
|================================================================ | 41% 166 MB
|================================================================ | 41% 166 MB
|================================================================ | 41% 167 MB
|================================================================ | 42% 167 MB
|================================================================ | 42% 168 MB
|================================================================= | 42% 168 MB
|================================================================= | 42% 168 MB
|================================================================= | 42% 169 MB
|================================================================= | 42% 169 MB
|================================================================= | 42% 170 MB
|================================================================= | 42% 170 MB
|================================================================== | 42% 171 MB
|================================================================== | 42% 171 MB
|================================================================== | 43% 171 MB
|================================================================== | 43% 172 MB
|================================================================== | 43% 172 MB
|================================================================== | 43% 173 MB
|================================================================== | 43% 173 MB
|=================================================================== | 43% 173 MB
|=================================================================== | 43% 174 MB
|=================================================================== | 43% 174 MB
|=================================================================== | 43% 175 MB
|=================================================================== | 44% 175 MB
|=================================================================== | 44% 175 MB
|==================================================================== | 44% 176 MB
|==================================================================== | 44% 176 MB
|==================================================================== | 44% 177 MB
|==================================================================== | 44% 177 MB
|==================================================================== | 44% 177 MB
|==================================================================== | 44% 178 MB
|==================================================================== | 44% 178 MB
|===================================================================== | 44% 179 MB
|===================================================================== | 44% 179 MB
|===================================================================== | 45% 179 MB
|===================================================================== | 45% 180 MB
|===================================================================== | 45% 180 MB
|===================================================================== | 45% 181 MB
|====================================================================== | 45% 181 MB
|====================================================================== | 45% 181 MB
|====================================================================== | 45% 182 MB
|====================================================================== | 45% 182 MB
|====================================================================== | 45% 183 MB
|====================================================================== | 46% 183 MB
|====================================================================== | 46% 183 MB
|======================================================================= | 46% 184 MB
|======================================================================= | 46% 184 MB
|======================================================================= | 46% 185 MB
|======================================================================= | 46% 185 MB
|======================================================================= | 46% 185 MB
|======================================================================= | 46% 186 MB
|======================================================================== | 46% 186 MB
|======================================================================== | 46% 187 MB
|======================================================================== | 46% 187 MB
|======================================================================== | 47% 187 MB
|======================================================================== | 47% 188 MB
|======================================================================== | 47% 188 MB
|======================================================================== | 47% 188 MB
|========================================================================= | 47% 189 MB
|========================================================================= | 47% 189 MB
|========================================================================= | 47% 190 MB
|========================================================================= | 47% 190 MB
|========================================================================= | 47% 190 MB
|========================================================================= | 47% 191 MB
|========================================================================== | 48% 191 MB
|========================================================================== | 48% 192 MB
|========================================================================== | 48% 192 MB
|========================================================================== | 48% 193 MB
|========================================================================== | 48% 193 MB
|========================================================================== | 48% 193 MB
|========================================================================== | 48% 194 MB
|=========================================================================== | 48% 194 MB
|=========================================================================== | 48% 194 MB
|=========================================================================== | 48% 195 MB
|=========================================================================== | 49% 195 MB
|=========================================================================== | 49% 196 MB
|=========================================================================== | 49% 196 MB
|============================================================================ | 49% 196 MB
|============================================================================ | 49% 197 MB
|============================================================================ | 49% 197 MB
|============================================================================ | 49% 198 MB
|============================================================================ | 49% 198 MB
|============================================================================ | 49% 199 MB
|============================================================================ | 49% 199 MB
|============================================================================= | 50% 199 MB
|============================================================================= | 50% 200 MB
|============================================================================= | 50% 200 MB
|============================================================================= | 50% 201 MB
|============================================================================= | 50% 201 MB
|============================================================================= | 50% 201 MB
|============================================================================== | 50% 202 MB
|============================================================================== | 50% 202 MB
|============================================================================== | 50% 203 MB
|============================================================================== | 50% 203 MB
|============================================================================== | 51% 203 MB
|============================================================================== | 51% 204 MB
|============================================================================== | 51% 204 MB
|=============================================================================== | 51% 204 MB
|=============================================================================== | 51% 205 MB
|=============================================================================== | 51% 205 MB
|=============================================================================== | 51% 206 MB
|=============================================================================== | 51% 206 MB
|=============================================================================== | 51% 206 MB
|================================================================================ | 51% 207 MB
|================================================================================ | 52% 207 MB
|================================================================================ | 52% 208 MB
|================================================================================ | 52% 208 MB
|================================================================================ | 52% 208 MB
|================================================================================ | 52% 209 MB
|================================================================================ | 52% 209 MB
|================================================================================= | 52% 210 MB
|================================================================================= | 52% 210 MB
|================================================================================= | 52% 210 MB
|================================================================================= | 52% 211 MB
|================================================================================= | 53% 211 MB
|================================================================================= | 53% 212 MB
|================================================================================== | 53% 212 MB
|================================================================================== | 53% 212 MB
|================================================================================== | 53% 213 MB
|================================================================================== | 53% 213 MB
|================================================================================== | 53% 213 MB
|================================================================================== | 53% 214 MB
|================================================================================== | 53% 214 MB
|=================================================================================== | 53% 215 MB
|=================================================================================== | 54% 215 MB
|=================================================================================== | 54% 216 MB
|=================================================================================== | 54% 216 MB
|=================================================================================== | 54% 216 MB
|=================================================================================== | 54% 217 MB
|=================================================================================== | 54% 217 MB
|==================================================================================== | 54% 217 MB
|==================================================================================== | 54% 218 MB
|==================================================================================== | 54% 218 MB
|==================================================================================== | 54% 219 MB
|==================================================================================== | 55% 219 MB
|==================================================================================== | 55% 219 MB
|===================================================================================== | 55% 220 MB
|===================================================================================== | 55% 220 MB
|===================================================================================== | 55% 221 MB
|===================================================================================== | 55% 221 MB
|===================================================================================== | 55% 221 MB
|===================================================================================== | 55% 222 MB
|===================================================================================== | 55% 222 MB
|====================================================================================== | 55% 223 MB
|====================================================================================== | 55% 223 MB
|====================================================================================== | 56% 223 MB
|====================================================================================== | 56% 224 MB
|====================================================================================== | 56% 224 MB
|====================================================================================== | 56% 224 MB
|====================================================================================== | 56% 225 MB
|======================================================================================= | 56% 225 MB
|======================================================================================= | 56% 226 MB
|======================================================================================= | 56% 226 MB
|======================================================================================= | 56% 226 MB
|======================================================================================= | 56% 227 MB
|======================================================================================= | 57% 227 MB
|======================================================================================== | 57% 228 MB
|======================================================================================== | 57% 228 MB
|======================================================================================== | 57% 228 MB
|======================================================================================== | 57% 229 MB
|======================================================================================== | 57% 229 MB
|======================================================================================== | 57% 230 MB
|======================================================================================== | 57% 230 MB
|========================================================================================= | 57% 230 MB
|========================================================================================= | 57% 231 MB
|========================================================================================= | 58% 231 MB
|========================================================================================= | 58% 232 MB
|========================================================================================= | 58% 232 MB
|========================================================================================= | 58% 232 MB
|========================================================================================= | 58% 233 MB
|========================================================================================== | 58% 233 MB
|========================================================================================== | 58% 233 MB
|========================================================================================== | 58% 234 MB
|========================================================================================== | 58% 234 MB
|========================================================================================== | 58% 235 MB
|========================================================================================== | 59% 235 MB
|=========================================================================================== | 59% 235 MB
|=========================================================================================== | 59% 236 MB
|=========================================================================================== | 59% 236 MB
|=========================================================================================== | 59% 237 MB
|=========================================================================================== | 59% 237 MB
|=========================================================================================== | 59% 237 MB
|=========================================================================================== | 59% 238 MB
|============================================================================================ | 59% 238 MB
|============================================================================================ | 59% 238 MB
|============================================================================================ | 59% 239 MB
|============================================================================================ | 60% 239 MB
|============================================================================================ | 60% 240 MB
|============================================================================================ | 60% 240 MB
|============================================================================================ | 60% 240 MB
|============================================================================================= | 60% 241 MB
|============================================================================================= | 60% 241 MB
|============================================================================================= | 60% 242 MB
|============================================================================================= | 60% 242 MB
|============================================================================================= | 60% 242 MB
|============================================================================================= | 60% 243 MB
|============================================================================================== | 61% 243 MB
|============================================================================================== | 61% 244 MB
|============================================================================================== | 61% 244 MB
|============================================================================================== | 61% 244 MB
|============================================================================================== | 61% 245 MB
|============================================================================================== | 61% 245 MB
|============================================================================================== | 61% 246 MB
|=============================================================================================== | 61% 246 MB
|=============================================================================================== | 61% 246 MB
|=============================================================================================== | 61% 247 MB
|=============================================================================================== | 62% 247 MB
|=============================================================================================== | 62% 248 MB
|=============================================================================================== | 62% 248 MB
|================================================================================================ | 62% 248 MB
|================================================================================================ | 62% 249 MB
|================================================================================================ | 62% 249 MB
|================================================================================================ | 62% 249 MB
|================================================================================================ | 62% 250 MB
|================================================================================================ | 62% 250 MB
|================================================================================================ | 62% 251 MB
|================================================================================================= | 63% 251 MB
|================================================================================================= | 63% 251 MB
|================================================================================================= | 63% 252 MB
|================================================================================================= | 63% 252 MB
|================================================================================================= | 63% 253 MB
|================================================================================================= | 63% 253 MB
|================================================================================================= | 63% 253 MB
|================================================================================================== | 63% 254 MB
|================================================================================================== | 63% 254 MB
|================================================================================================== | 63% 255 MB
|================================================================================================== | 64% 255 MB
|================================================================================================== | 64% 255 MB
|================================================================================================== | 64% 256 MB
|=================================================================================================== | 64% 256 MB
|=================================================================================================== | 64% 256 MB
|=================================================================================================== | 64% 257 MB
|=================================================================================================== | 64% 257 MB
|=================================================================================================== | 64% 258 MB
|=================================================================================================== | 64% 258 MB
|=================================================================================================== | 64% 258 MB
|==================================================================================================== | 64% 259 MB
|==================================================================================================== | 65% 259 MB
|==================================================================================================== | 65% 260 MB
|==================================================================================================== | 65% 260 MB
|==================================================================================================== | 65% 260 MB
|==================================================================================================== | 65% 261 MB
|===================================================================================================== | 65% 261 MB
|===================================================================================================== | 65% 262 MB
|===================================================================================================== | 65% 262 MB
|===================================================================================================== | 65% 262 MB
|===================================================================================================== | 65% 263 MB
|===================================================================================================== | 66% 263 MB
|===================================================================================================== | 66% 264 MB
|====================================================================================================== | 66% 264 MB
|====================================================================================================== | 66% 264 MB
|====================================================================================================== | 66% 265 MB
|====================================================================================================== | 66% 265 MB
|====================================================================================================== | 66% 265 MB
|====================================================================================================== | 66% 266 MB
|====================================================================================================== | 66% 266 MB
|======================================================================================================= | 66% 267 MB
|======================================================================================================= | 67% 267 MB
|======================================================================================================= | 67% 267 MB
|======================================================================================================= | 67% 268 MB
|======================================================================================================= | 67% 268 MB
|======================================================================================================= | 67% 269 MB
|======================================================================================================== | 67% 269 MB
|======================================================================================================== | 67% 269 MB
|======================================================================================================== | 67% 270 MB
|======================================================================================================== | 67% 270 MB
|======================================================================================================== | 67% 271 MB
|======================================================================================================== | 68% 271 MB
|======================================================================================================== | 68% 271 MB
|========================================================================================================= | 68% 272 MB
|========================================================================================================= | 68% 272 MB
|========================================================================================================= | 68% 273 MB
|========================================================================================================= | 68% 273 MB
|========================================================================================================= | 68% 273 MB
|========================================================================================================= | 68% 274 MB
|========================================================================================================= | 68% 274 MB
|========================================================================================================== | 68% 274 MB
|========================================================================================================== | 69% 275 MB
|========================================================================================================== | 69% 275 MB
|========================================================================================================== | 69% 276 MB
|========================================================================================================== | 69% 276 MB
|========================================================================================================== | 69% 277 MB
|=========================================================================================================== | 69% 277 MB
|=========================================================================================================== | 69% 277 MB
|=========================================================================================================== | 69% 278 MB
|=========================================================================================================== | 69% 278 MB
|=========================================================================================================== | 69% 279 MB
|=========================================================================================================== | 70% 279 MB
|=========================================================================================================== | 70% 279 MB
|============================================================================================================ | 70% 280 MB
|============================================================================================================ | 70% 280 MB
|============================================================================================================ | 70% 280 MB
|============================================================================================================ | 70% 281 MB
|============================================================================================================ | 70% 281 MB
|============================================================================================================ | 70% 282 MB
|============================================================================================================= | 70% 282 MB
|============================================================================================================= | 70% 282 MB
|============================================================================================================= | 71% 283 MB
|============================================================================================================= | 71% 283 MB
|============================================================================================================= | 71% 284 MB
|============================================================================================================= | 71% 284 MB
|============================================================================================================= | 71% 284 MB
|============================================================================================================== | 71% 285 MB
|============================================================================================================== | 71% 285 MB
|============================================================================================================== | 71% 285 MB
|============================================================================================================== | 71% 286 MB
|============================================================================================================== | 71% 286 MB
|============================================================================================================== | 71% 287 MB
|============================================================================================================== | 72% 287 MB
|=============================================================================================================== | 72% 287 MB
|=============================================================================================================== | 72% 288 MB
|=============================================================================================================== | 72% 288 MB
|=============================================================================================================== | 72% 289 MB
|=============================================================================================================== | 72% 289 MB
|=============================================================================================================== | 72% 289 MB
|================================================================================================================ | 72% 290 MB
|================================================================================================================ | 72% 290 MB
|================================================================================================================ | 72% 290 MB
|================================================================================================================ | 73% 291 MB
|================================================================================================================ | 73% 291 MB
|================================================================================================================ | 73% 292 MB
|================================================================================================================ | 73% 292 MB
|================================================================================================================= | 73% 292 MB
|================================================================================================================= | 73% 293 MB
|================================================================================================================= | 73% 293 MB
|================================================================================================================= | 73% 294 MB
|================================================================================================================= | 73% 294 MB
|================================================================================================================= | 73% 294 MB
|================================================================================================================== | 74% 295 MB
|================================================================================================================== | 74% 295 MB
|================================================================================================================== | 74% 296 MB
|================================================================================================================== | 74% 296 MB
|================================================================================================================== | 74% 296 MB
|================================================================================================================== | 74% 297 MB
|================================================================================================================== | 74% 297 MB
|=================================================================================================================== | 74% 298 MB
|=================================================================================================================== | 74% 298 MB
|=================================================================================================================== | 74% 298 MB
|=================================================================================================================== | 74% 299 MB
|=================================================================================================================== | 75% 299 MB
|=================================================================================================================== | 75% 299 MB
|=================================================================================================================== | 75% 300 MB
|==================================================================================================================== | 75% 300 MB
|==================================================================================================================== | 75% 301 MB
|==================================================================================================================== | 75% 301 MB
|==================================================================================================================== | 75% 301 MB
|==================================================================================================================== | 75% 302 MB
|==================================================================================================================== | 75% 302 MB
|==================================================================================================================== | 75% 303 MB
|===================================================================================================================== | 76% 303 MB
|===================================================================================================================== | 76% 303 MB
|===================================================================================================================== | 76% 304 MB
|===================================================================================================================== | 76% 304 MB
|===================================================================================================================== | 76% 304 MB
|===================================================================================================================== | 76% 305 MB
|====================================================================================================================== | 76% 305 MB
|====================================================================================================================== | 76% 306 MB
|====================================================================================================================== | 76% 306 MB
|====================================================================================================================== | 76% 306 MB
|====================================================================================================================== | 77% 307 MB
|====================================================================================================================== | 77% 307 MB
|====================================================================================================================== | 77% 308 MB
|======================================================================================================================= | 77% 308 MB
|======================================================================================================================= | 77% 308 MB
|======================================================================================================================= | 77% 309 MB
|======================================================================================================================= | 77% 309 MB
|======================================================================================================================= | 77% 310 MB
|======================================================================================================================= | 77% 310 MB
|======================================================================================================================== | 77% 310 MB
|======================================================================================================================== | 78% 311 MB
|======================================================================================================================== | 78% 311 MB
|======================================================================================================================== | 78% 312 MB
|======================================================================================================================== | 78% 312 MB
|======================================================================================================================== | 78% 312 MB
|======================================================================================================================== | 78% 313 MB
|========================================================================================================================= | 78% 313 MB
|========================================================================================================================= | 78% 313 MB
|========================================================================================================================= | 78% 314 MB
|========================================================================================================================= | 78% 314 MB
|========================================================================================================================= | 78% 315 MB
|========================================================================================================================= | 79% 315 MB
|========================================================================================================================= | 79% 315 MB
|========================================================================================================================== | 79% 316 MB
|========================================================================================================================== | 79% 316 MB
|========================================================================================================================== | 79% 317 MB
|========================================================================================================================== | 79% 317 MB
|========================================================================================================================== | 79% 317 MB
|========================================================================================================================== | 79% 318 MB
|========================================================================================================================== | 79% 318 MB
|=========================================================================================================================== | 79% 319 MB
|=========================================================================================================================== | 80% 319 MB
|=========================================================================================================================== | 80% 319 MB
|=========================================================================================================================== | 80% 320 MB
|=========================================================================================================================== | 80% 320 MB
|=========================================================================================================================== | 80% 320 MB
|============================================================================================================================ | 80% 321 MB
|============================================================================================================================ | 80% 321 MB
|============================================================================================================================ | 80% 322 MB
|============================================================================================================================ | 80% 322 MB
|============================================================================================================================ | 80% 322 MB
|============================================================================================================================ | 81% 323 MB
|============================================================================================================================ | 81% 323 MB
|============================================================================================================================= | 81% 324 MB
|============================================================================================================================= | 81% 324 MB
|============================================================================================================================= | 81% 324 MB
|============================================================================================================================= | 81% 325 MB
|============================================================================================================================= | 81% 325 MB
|============================================================================================================================= | 81% 326 MB
|============================================================================================================================== | 81% 326 MB
|============================================================================================================================== | 81% 326 MB
|============================================================================================================================== | 82% 327 MB
|============================================================================================================================== | 82% 327 MB
|============================================================================================================================== | 82% 328 MB
|============================================================================================================================== | 82% 328 MB
|============================================================================================================================== | 82% 328 MB
|=============================================================================================================================== | 82% 329 MB
|=============================================================================================================================== | 82% 329 MB
|=============================================================================================================================== | 82% 330 MB
|=============================================================================================================================== | 82% 330 MB
|=============================================================================================================================== | 82% 330 MB
|=============================================================================================================================== | 83% 331 MB
|================================================================================================================================ | 83% 331 MB
|================================================================================================================================ | 83% 332 MB
|================================================================================================================================ | 83% 332 MB
|================================================================================================================================ | 83% 332 MB
|================================================================================================================================ | 83% 333 MB
|================================================================================================================================ | 83% 333 MB
|================================================================================================================================ | 83% 333 MB
|================================================================================================================================= | 83% 334 MB
|================================================================================================================================= | 83% 334 MB
|================================================================================================================================= | 83% 335 MB
|================================================================================================================================= | 84% 335 MB
|================================================================================================================================= | 84% 335 MB
|================================================================================================================================= | 84% 336 MB
|================================================================================================================================= | 84% 336 MB
|================================================================================================================================== | 84% 337 MB
|================================================================================================================================== | 84% 337 MB
|================================================================================================================================== | 84% 337 MB
|================================================================================================================================== | 84% 338 MB
|================================================================================================================================== | 84% 338 MB
|================================================================================================================================== | 84% 339 MB
|=================================================================================================================================== | 85% 339 MB
|=================================================================================================================================== | 85% 339 MB
|=================================================================================================================================== | 85% 340 MB
|=================================================================================================================================== | 85% 340 MB
|=================================================================================================================================== | 85% 341 MB
|=================================================================================================================================== | 85% 341 MB
|=================================================================================================================================== | 85% 341 MB
|==================================================================================================================================== | 85% 342 MB
|==================================================================================================================================== | 85% 342 MB
|==================================================================================================================================== | 85% 343 MB
|==================================================================================================================================== | 86% 343 MB
|==================================================================================================================================== | 86% 343 MB
|==================================================================================================================================== | 86% 344 MB
|===================================================================================================================================== | 86% 344 MB
|===================================================================================================================================== | 86% 345 MB
|===================================================================================================================================== | 86% 345 MB
|===================================================================================================================================== | 86% 345 MB
|===================================================================================================================================== | 86% 346 MB
|===================================================================================================================================== | 86% 346 MB
|===================================================================================================================================== | 86% 346 MB
|====================================================================================================================================== | 87% 347 MB
|====================================================================================================================================== | 87% 347 MB
|====================================================================================================================================== | 87% 348 MB
|====================================================================================================================================== | 87% 348 MB
|====================================================================================================================================== | 87% 348 MB
|====================================================================================================================================== | 87% 349 MB
|====================================================================================================================================== | 87% 349 MB
|======================================================================================================================================= | 87% 349 MB
|======================================================================================================================================= | 87% 350 MB
|======================================================================================================================================= | 87% 350 MB
|======================================================================================================================================= | 88% 351 MB
|======================================================================================================================================= | 88% 351 MB
|======================================================================================================================================= | 88% 351 MB
|======================================================================================================================================= | 88% 352 MB
|======================================================================================================================================== | 88% 352 MB
|======================================================================================================================================== | 88% 352 MB
|======================================================================================================================================== | 88% 353 MB
|======================================================================================================================================== | 88% 353 MB
|======================================================================================================================================== | 88% 354 MB
|======================================================================================================================================== | 88% 354 MB
|======================================================================================================================================== | 88% 354 MB
|========================================================================================================================================= | 89% 355 MB
|========================================================================================================================================= | 89% 355 MB
|========================================================================================================================================= | 89% 355 MB
|========================================================================================================================================= | 89% 356 MB
|========================================================================================================================================= | 89% 356 MB
|========================================================================================================================================= | 89% 357 MB
|========================================================================================================================================= | 89% 357 MB
|========================================================================================================================================== | 89% 357 MB
|========================================================================================================================================== | 89% 358 MB
|========================================================================================================================================== | 89% 358 MB
|========================================================================================================================================== | 89% 358 MB
|========================================================================================================================================== | 90% 359 MB
|========================================================================================================================================== | 90% 359 MB
|========================================================================================================================================== | 90% 359 MB
|=========================================================================================================================================== | 90% 360 MB
|=========================================================================================================================================== | 90% 360 MB
|=========================================================================================================================================== | 90% 360 MB
|=========================================================================================================================================== | 90% 361 MB
|=========================================================================================================================================== | 90% 361 MB
|=========================================================================================================================================== | 90% 362 MB
|=========================================================================================================================================== | 90% 362 MB
|============================================================================================================================================ | 90% 362 MB
|============================================================================================================================================ | 91% 363 MB
|============================================================================================================================================ | 91% 363 MB
|============================================================================================================================================ | 91% 364 MB
|============================================================================================================================================ | 91% 364 MB
|============================================================================================================================================ | 91% 364 MB
|============================================================================================================================================ | 91% 365 MB
|============================================================================================================================================= | 91% 365 MB
|============================================================================================================================================= | 91% 366 MB
|============================================================================================================================================= | 91% 366 MB
|============================================================================================================================================= | 91% 366 MB
|============================================================================================================================================= | 92% 367 MB
|============================================================================================================================================= | 92% 367 MB
|============================================================================================================================================== | 92% 367 MB
|============================================================================================================================================== | 92% 368 MB
|============================================================================================================================================== | 92% 368 MB
|============================================================================================================================================== | 92% 369 MB
|============================================================================================================================================== | 92% 369 MB
|============================================================================================================================================== | 92% 369 MB
|============================================================================================================================================== | 92% 370 MB
|=============================================================================================================================================== | 92% 370 MB
|=============================================================================================================================================== | 92% 370 MB
|=============================================================================================================================================== | 93% 371 MB
|=============================================================================================================================================== | 93% 371 MB
|=============================================================================================================================================== | 93% 372 MB
|=============================================================================================================================================== | 93% 372 MB
|=============================================================================================================================================== | 93% 372 MB
|================================================================================================================================================ | 93% 373 MB
|================================================================================================================================================ | 93% 373 MB
|================================================================================================================================================ | 93% 373 MB
|================================================================================================================================================ | 93% 374 MB
|================================================================================================================================================ | 93% 374 MB
|================================================================================================================================================ | 93% 374 MB
|================================================================================================================================================ | 94% 375 MB
|================================================================================================================================================ | 94% 375 MB
|================================================================================================================================================= | 94% 375 MB
|================================================================================================================================================= | 94% 376 MB
|================================================================================================================================================= | 94% 376 MB
|================================================================================================================================================= | 94% 377 MB
|================================================================================================================================================= | 94% 377 MB
|================================================================================================================================================= | 94% 377 MB
|================================================================================================================================================= | 94% 378 MB
|================================================================================================================================================== | 94% 378 MB
|================================================================================================================================================== | 94% 378 MB
|================================================================================================================================================== | 95% 379 MB
|================================================================================================================================================== | 95% 379 MB
|================================================================================================================================================== | 95% 379 MB
|================================================================================================================================================== | 95% 380 MB
|================================================================================================================================================== | 95% 380 MB
|=================================================================================================================================================== | 95% 380 MB
|=================================================================================================================================================== | 95% 381 MB
|=================================================================================================================================================== | 95% 381 MB
|=================================================================================================================================================== | 95% 382 MB
|=================================================================================================================================================== | 95% 382 MB
|=================================================================================================================================================== | 95% 382 MB
|=================================================================================================================================================== | 95% 383 MB
|=================================================================================================================================================== | 96% 383 MB
|==================================================================================================================================================== | 96% 383 MB
|==================================================================================================================================================== | 96% 384 MB
|==================================================================================================================================================== | 96% 384 MB
|==================================================================================================================================================== | 96% 384 MB
|==================================================================================================================================================== | 96% 385 MB
|==================================================================================================================================================== | 96% 385 MB
|==================================================================================================================================================== | 96% 385 MB
|===================================================================================================================================================== | 96% 386 MB
|===================================================================================================================================================== | 96% 386 MB
|===================================================================================================================================================== | 96% 386 MB
|===================================================================================================================================================== | 97% 387 MB
|===================================================================================================================================================== | 97% 387 MB
|===================================================================================================================================================== | 97% 387 MB
|===================================================================================================================================================== | 97% 388 MB
|===================================================================================================================================================== | 97% 388 MB
|====================================================================================================================================================== | 97% 388 MB
|====================================================================================================================================================== | 97% 389 MB
|====================================================================================================================================================== | 97% 389 MB
|====================================================================================================================================================== | 97% 389 MB
|====================================================================================================================================================== | 97% 390 MB
|====================================================================================================================================================== | 97% 390 MB
|====================================================================================================================================================== | 97% 390 MB
|====================================================================================================================================================== | 98% 391 MB
|======================================================================================================================================================= | 98% 391 MB
|======================================================================================================================================================= | 98% 391 MB
|======================================================================================================================================================= | 98% 392 MB
|======================================================================================================================================================= | 98% 392 MB
|======================================================================================================================================================= | 98% 392 MB
|======================================================================================================================================================= | 98% 393 MB
|======================================================================================================================================================= | 98% 393 MB
|======================================================================================================================================================== | 98% 393 MB
|======================================================================================================================================================== | 98% 394 MB
|======================================================================================================================================================== | 98% 394 MB
|======================================================================================================================================================== | 98% 394 MB
|======================================================================================================================================================== | 99% 395 MB
|======================================================================================================================================================== | 99% 395 MB
|======================================================================================================================================================== | 99% 395 MB
|======================================================================================================================================================== | 99% 396 MB
|=========================================================================================================================================================| 99% 396 MB
|=========================================================================================================================================================| 99% 396 MB
|=========================================================================================================================================================| 99% 397 MB
|=========================================================================================================================================================| 99% 397 MB
|=========================================================================================================================================================| 99% 397 MB
|=========================================================================================================================================================| 99% 398 MB
|=========================================================================================================================================================| 99% 398 MB
|=========================================================================================================================================================| 99% 398 MB
|==========================================================================================================================================================| 100% 398 MB
snps
filter to keep snps where there is data from all samples
snps <- snps %>%
filter({select(., matches("[0-9]")) %>% complete.cases() })
snps
snps <- snps %>%
filter(QUAL >=50,
nchar(ALT)==1)
snps